adephylo-package {adephylo}R Documentation

The adephylo package

Description

This package is devoted to exploratory analysis of phylogenetic comparative data. It re-implements and extends phylogenetic procedures from the ade4 package (which are now deprecated).

Details

Comparative data (phylogeny+traits) are handled as phylo4d objects, a canonical class implemented by the phylobase package. Trees are handled as phylo objects (from the ape package) or as phylo4 objects (phylobase's extension of phylo objects).

Main functionalities of adephylo are summarized below.

=== TOPOLOGICAL INFORMATION ===
Several functions allow one to retrieve topological information from a tree; such information can be used, for instance, as a basis to compute distances or proximities between tips.

- listDD: lists the direct descendants from each node of a tree.

- listTips: lists the tips descending from each node of a tree.

- .tipToRoot: finds the set of nodes between a tip and the root of a tree.

- sp.tips: finds the shortest path between tips of a tree.

- treePart: defines partitions of tips reflecting the topology of a tree. This function can output non-independent dummy vectors, or alternatively an orthonormal basis used by the orthogram procedure.

=== PHYLOGENETIC PROXIMITIES/DISTANCES ===
Several phylogenetic proximities and distances are implemented. Auxiliary function easing the computation of other distances/proximities are also provided:

- distRoot: computes different distances of a set of tips to the root.

- distTips: computes different pairwise distances in a set of tips.

- proxTips: computes different proximities between a set of tips.

=== MEASURES/TESTS OF PHYLOGENETIC AUTOCORRELATION ===
Several procedures allow one to measure, and/or test phylogenetic signal in biological traits:

- abouheif.moran: performs Abouheif's test, designed to detect phylogenetic autocorrelation in a quantitative trait. This implementation is not based on original heuristic procedure, but on the exact formulation proposed by Pavoine et al. (2008), showing that the test is in fact a Moran's index test. This implementation further extends the procedure by allowing any measure of phylogenetic proximity (5 are proposed).

- orthogram: performs the orthonormal decomposition of variance of a quantitative variable on an orthonormal basis as in Ollier et al. (2005). It also returns the results of five non parametric tests associated to the variance decomposition.

- moran.idx: computes Moran's index of autocorrelation given a variable and a matrix of proximities among observations (no test).

=== MODELLING/INVESTIGATION OF PHYLOGENETIC SIGNAL ===
Rather than testing or measuring phylogenetic autocorrelation, these procedures can be used for further investigation of phylogenetic signal. Some, like me.phylo, can be used to remove phylogenetic autocorrelation. Others can be used to understand the nature of this autocorrelation (i.e., to ascertain which traits and tips are concerned by phylogenetic non-independence).

- me.phylo/orthobasis.phylo: these synonymous functions compute Moran's eigenvectors (ME) associated to a tree. These vectors model different observable phylogenetic signals. They can be used as covariables to remove phylogenetic autocorrelation from data.

- orthogram: the orthogram mentioned above also provides a description of how biological variability is structured on a phylogeny.

- ppca: performs a phylogenetic Principal Component Analysis (pPCA, Jombart et al. 2010). This multivariate method investigates phylogenetic patterns in a set of quantitative traits.

=== GRAPHICS ===
Some plotting functions are proposed, most of them being devoted to representing phylogeny and a quantitative information at the same time.

- table.phylo4d: fairly customisable way of representing traits onto the tips of a phylogeny. Several traits can be plotted in a single graphic.

- bullseye: an alternative to table.phylo4d based on fan-like representation, better for large trees.

- scatter.ppca, screeplot.ppca, plot.ppca: several plots associated to a phylogenetic principal component analysis (see ppca).

=== DATASETS ===
Several datasets are also proposed. Some of these datasets replace former version from ade4, which are now deprecated. Here is a list of available datasets: carni19, carni70, lizards, maples, mjrochet, palm, procella, tithonia, and ungulates.

To cite adephylo, please use the reference given by citation("adephylo").

Package: adephylo
Type: Package
Version: 1.1-7
Date: 2014-11-10
License: GPL (>=2)

Author(s)

Thibaut Jombart <tjombart@imperial.ac.uk>
with contributions Stephane Dray <stephane.dray@univ-lyon1.fr> and Anders Ellern Bilgrau <abilgrau@math.aau.dk>.
Parts of former code from ade4 by Daniel Chessel and Sebastien Ollier.

See Also

The ade4 package for multivariate analysis.


[Package adephylo version 1.1-11 Index]